Human bocavirus

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Human bocavirus
Scientific classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Monodnaviria
Kingdom: Shotokuvirae
Phylum: Cossaviricota
Class: Quintoviricetes
Order: Piccovirales
Family: Parvoviridae
Subfamily: Parvovirinae
Genus: Bocaparvovirus
Groups included
Member viruses [1]
Cladistically included but traditionally excluded taxa

All other viruses and strains in species:

Human bocavirus (HBoV) is the name given to all viruses in the genus Bocaparvovirus of virus family Parvoviridae [2] that are known to infect humans. HBoV1 and HBoV3 (and gorilla bocaparvovirus) are members of species Primate bocaparvovirus 1 whereas viruses HBoV2 and HBoV4 belong to species Primate bocaparvovirus 2 . Some of these viruses cause human disease. HBoV1 is strongly implicated in causing some cases of lower respiratory tract infection, especially in young children, and several of the viruses have been linked to gastroenteritis, although the full clinical role of this emerging infectious disease remains to be elucidated.

Contents

History

Allander and colleagues at the Karolinska Institutet in Stockholm, Sweden, first cloned the coding sequence of this new member of the family of Parvoviridae in 2005 from pooled nasopharyngeal aspirates (NPA, collection of aspirated fluid from the back of the nasal cavity). [3] They used a novel technique called molecular virus screening, based on random cloning and bioinformatical analysis. This technique has led to the discovery of new viruses such as polyomavirus KI (Karolinska Institute) [4] and WU (Washington University), [5] which are closely related to each other and have been isolated from respiratory secretions.

Several groups of scientists have since then found that HBoV is the fourth most common virus in respiratory samples, [6] [7] behind rhinoviruses, respiratory syncytial virus, and adenoviruses. [8]

The name bocavirus is derived from bovine and canine, referring to the two known hosts for the founder members of this genus; bovine parvovirus which infects cattle, and minute virus of canines which infects dogs. [9] Parvoviruses (Latin: small viruses) have a 5 kilobase long single-stranded DNA, and they use some of their host's replication proteins to copy their DNA.

Virology

The virions are small (diameter 18–26 nanometers), icosahedral and non enveloped. The capsid has T = 1 symmetry and consists of 60 copies of coat protein. The coat proteins have a conserved, eight stranded beta barrel motif that forms the core of the capsid. There is also a conserved alpha helix. [10]

The HBoV capsid shares three characteristic features also found in the other vertebrate parvoviruses: [10] (1) a dimple like depression at each icosahedral 2-fold axis; (2) a large trimeric protrusion at or surrounding each 3-fold axis; (3) a cylindrical projection surrounding each 5-fold axis that encloses a central channel which connects the inside of the particle with its exterior and serves as the entry and exit portal for viral DNA. This 5-fold cylinder is itself encircled by a wide canyon like depression. While the dimple is also found among the invertebrate parvoviruses, they typically lack the 3-fold protrusions and canyon around the 5-fold channel. The external diameter of the capsid ranges from ~21.5  nanometers (nm) at the lowest points of the dimple and canyon to ~28 nm at the top of the protrusion.

The genome is a linear, single-stranded DNA 5.5 kilobases in length with disparate terminal hairpin structures at each end.

The genome encodes 3 open reading frames (ORF1, 2 and 3). The left ORF encodes 4 non structural proteins (NS1, NS2, NS3 and NS4). The middle ORF encodes NP1. The right hand ORF (ORF3) encodes the capsid proteins (VP1, VP2, and VP3). The NP1 gene is in an alternate reading frame to VP1 and overlaps the start of VP1 by 13 nucleotides. Similarly, VP3 is collinear to VP1 and VP2 and results from initiation of translation at a downstream ATG and co-terminates. VP2 is translated from a non-canonical start codon GUG.

A viral noncoding RNA of 140 nucleotides, named as bocavirus-encoded small RNA (BocaSR), is expressed from the 3' noncoding region after the VP ORF.

NP1 is a small non-structural protein that could induce apoptosis in transfection of HeLa cells. [11]

There is a single promoter located within the 3' hairpin. This is responsible for, by alternative splicing and alternative polyadenylation, for the generation of several (at least 6) mRNAs. [12] The poly A tail is about 150 nucleotides in length.

After nuclear import the single stranded genome is converted to double stranded DNA and production of the viral NS1 protein commences.

The genome is replicated through a unique linear rolling hairpin mechanism that is dependent on the NS1 protein. [13] Replication has been reported to result in the creation of a series of circular head to tail sequences. [14]

A sequence conserved among the Parvoviridae TAAAAAT is found close to the 3' terminus.

Other parvoviruses replicate only when the host cell is in S phase: viral replication results in the death of the host cell. This pattern has not yet been experimentally confirmed for the bocaviruses but seems likely to be the case. Expression of the viral proteins alone does not cause host cell death unlike other parvoviruses where this has been examined. [15]

Molecular biology

Parvoviral rolling hairpin replication is a linear adaptation of the rolling-circle replication (RCR) mechanisms used by many small plasmids and viruses. NS1, the multifunctional viral replication initiation protein, forms an oligomeric multidomain molecule that has both site- and strand-specific HuH endonuclease and superfamily III (SF3) helicase activity. All SF3 helicases travel along DNA in a 3′-to-5′ direction. Four conserved sequence motifs are found in SF3 helicases (A, B, B′, and C). These motifs form the nucleoside triphosphate binding pocket, the metal ion coordination site, the DNA-binding site and the sensory element. These motifs are in a stretch of approximately 100 amino acid residues in the middle of NS1. These helicases surround DNA as a ring of six or eight subunits with the ATP binding pocket lying between adjacent subunits. The first subunit provides the A and B motifs, and the arginine residue of the second subunit functions as a trans-acting arginine finger sensor for ATP binding and hydrolysis status. The arginine finger lies after the C motif but in three dimensions it is often embedded in a cluster of positively charged amino acids. In a ring configuration this domain interacts with the ATP binding pocket of the neighboring subunit.

The atomic structure of the HuH endonuclease domain of HBoV1 NS1 [16] closely resembles the nickase structures encoded by other parvoviruses and by more-distant RCR replicons. This structure also mediates site-specific duplex DNA-recognition, which allows NS1 to bind site-specifically to viral replication origins positioned at each end of its genome (derived from the sequences of the viral hairpin telomeres). Origin recognition, which for some parvoviruses must be enhanced by the binding of additional cellular cofactors, leads to strand- and site-specific nicking of viral duplex DNA replication intermediates, processes that require ATP for tight binding and subsequent nicking. The NS1 protein remains covalently linked to the 5′ end of nicked DNA, while the new 3′-hydroxyl group is able to prime synthesis of additional linear sequences. Replication of the genome is thought to be mediated by DNA repair DNA polymerases. This process involves the single strand-binding protein replication protein A and NS1. In this process, NS1 acts as an ATP powered helicase to resolve terminal hairpin structures of the viral genome.

NS1 is also responsible for the cytopathic effect of some parvoviruses, and there is evidence to indicate that some form of this protein associates with one of the 5-fold cylinders of newly assembled capsids where it serves as a molecular motor, using its 3'-to-5' helicase activity to drive the encapsidation of progeny single stranded DNA into the particle. [17]

Genetics

There are four known human genotypes of this virus: type 1 to 4. Types 1 and 2 appear to have diverged recently (circa 1985) [18] The estimated mean evolutionary rate is 8.6×10−4 substitutions/site/year. The 1st + 2nd codon positions evolve 15 times more slowly than those of the 3rd codon position.

There is 78%, 67%, and 80% identity between Human Bocavirus 1 and 2 NS1, NP1, and VP1/VP2 proteins respectively. [19] Recombination may occur between strains. Human bocavirus 3 appears to be a recombinant of human bocavirus 1 and a common ancestor of human bocaviruses 2 and 4. [20]

Bocaviruses have been isolated from pigs. [21] Phylogenetic analysis of swine bocavirus places it with canine minute virus. [22]

Incomplete sequences of bocaviruses have been obtained from wild chimpanzees. [23] These sequences phylogenetically lie within the known human bocavirus isolates but also show evidence of recombination.

Clinical

Chest radiograph of a 16-month-old boy in Finland with human bocavirus 1 pneumonia, on day 2 of hospitalization. Bilateral pulmonary infiltrations and atelectasis of the upper right lobe can be seen. Human bocavirus 1 pneumonia.jpg
Chest radiograph of a 16-month-old boy in Finland with human bocavirus 1 pneumonia, on day 2 of hospitalization. Bilateral pulmonary infiltrations and atelectasis of the upper right lobe can be seen.

HBoV is found in respiratory samples from healthy subjects. [24] In patients with respiratory complaints, it can be found alone or, more often, in combination with other viruses known to cause respiratory complaints. [6] Newborns are probably protected by passive immunization. [25] The age group most frequently affected appear to be children between the ages of six months to two years, [25] [26] although cases in children older than five and even in a 28-year-old have been reported. [27]

HBoV can be detected not only in respiratory samples but also in blood, urine, and stools. The latter two may merely reflect viral shedding, although diarrhea has been described in animal bocaviral infections, and some patients with HBoV seem to have diarrhea independent of respiratory symptoms. [28] [29]

A study in Jordan found that 9% of 220 children hospitalized with lower respiratory tract infection were infected with bocavirus. [30] Of those infected the median age was 4 months. Coughing (100%), wheezing (82.7%) and fever (68.2%) were the most common clinical findings with bronchopneumonia (35%) and bronchiolitis (30%) being the most common ultimate diagnoses.

HBoV1 has been generally associated with respiratory symptoms while other HBoV types tend to be associated with diarrhea and acute flaccid paralysis.

Although most cases are mild, severe respiratory disease has also been reported. [31]

Life-threatening infection caused by human bocavirus was described in previously healthy 20-months old prematurely born child. [32]

Related Research Articles

<span class="mw-page-title-main">DNA virus</span> Virus that has DNA as its genetic material

A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.

<i>Parvoviridae</i> Family of viruses

Parvoviruses are a family of animal viruses that constitute the family Parvoviridae. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the protein the viral capsid is made of. The coding portion of the genome is flanked by telomeres at each end that form into hairpin loops that are important during replication. Parvovirus virions are small compared to most viruses, at 23–28 nanometers in diameter, and contain the genome enclosed in an icosahedral capsid that has a rugged surface.

<span class="mw-page-title-main">Parvovirus B19</span> Human virus that infects RBC precursors.

Primate erythroparvovirus 1, generally referred to as B19 virus(B19V),parvovirus B19 or sometimes erythrovirus B19, is the first known human virus in the family Parvoviridae, genus Erythroparvovirus; it measures only 23–26 nm in diameter. The name is derived from Latin parvum, meaning small, reflecting the fact that B19 ranks among the smallest DNA viruses. B19 virus is most known for causing disease in the pediatric population; however, it can also affect adults. It is the classic cause of the childhood rash called fifth disease or erythema infectiosum, or "slapped cheek syndrome".

<i>Polyomaviridae</i> Family of viruses

Polyomaviridae is a family of viruses whose natural hosts are primarily mammals and birds. As of 2020, there are six recognized genera and 117 species, five of which are unassigned to a genus. 14 species are known to infect humans, while others, such as Simian Virus 40, have been identified in humans to a lesser extent. Most of these viruses are very common and typically asymptomatic in most human populations studied. BK virus is associated with nephropathy in renal transplant and non-renal solid organ transplant patients, JC virus with progressive multifocal leukoencephalopathy, and Merkel cell virus with Merkel cell cancer.

<span class="mw-page-title-main">Canine parvovirus</span> Contagious virus mainly affecting dogs

Canine parvovirus is a contagious virus mainly affecting dogs. CPV is highly contagious and is spread from dog to dog by direct or indirect contact with their feces. Vaccines can prevent this infection, but mortality can reach 91% in untreated cases. Treatment often involves veterinary hospitalization. Canine parvovirus often infects other mammals including foxes, wolves, cats, and skunks. Felines (cats) are also susceptible to panleukopenia, a different strain of parvovirus.

Porcine parvovirus (PPV), a virus in the species Ungulate protoparvovirus 1 of genus Protoparvovirus in the virus family Parvoviridae, causes reproductive failure of swine characterized by embryonic and fetal infection and death, usually in the absence of outward maternal clinical signs. The disease develops mainly when seronegative dams are exposed oronasally to the virus anytime during about the first half of gestation, and conceptuses are subsequently infected transplacentally before they become immunocompetent. There is no definitive evidence that infection of swine other than during gestation is of any clinical or economic significance. The virus is ubiquitous among swine throughout the world and is enzootic in most herds that have been tested. Diagnostic surveys have indicated that PPV is the major infectious cause of embryonic and fetal death. In addition to its direct causal role in reproductive failure, PPV can potentiate the effects of porcine circovirus type II (PCV2) infection in the clinical course of postweaning multisystemic wasting syndrome (PMWS).

Amdoparvovirus is a genus of viruses in the family Parvoviridae in the subfamily Parvovirinae. Mustelids, skunk, and raccoons serve as natural hosts. There are five species in this genus. Diseases associated with this genus include progressive disorder of immune system.

Carnivore bocaparvovirus 1, formerly Canine minute virus is a species of Bocaparvovirus of the family Parvoviridae that infects dogs. It is similar to bovine parvovirus in its protein structure and DNA. A virus causing respiratory disease in humans has been called human bocavirus due to its similarity to these viruses. Canine minute virus was originally discovered in Germany in 1967 in military dogs, although it was originally thought to not cause disease. Dogs and puppies are infected orally, and the virus is spread transplacentally to the fetuses. Symptoms are seen most commonly between the ages of one to three weeks and include severe diarrhea, difficulty breathing, and anorexia. In severe cases, illness can be fatal.

A helper dependent virus, also termed a gutless virus, is a synthetic viral vector dependent on the assistance of a helper virus in order to replicate, and can be used for purposes such as gene therapy. Naturally-occurring satellite viruses are also helper virus dependent, and can sometimes be modified to become viral vectors.

Visna-maedi virus from the genus Lentivirus and subfamily Orthoretrovirinae, is a retrovirus that causes encephalitis and chronic pneumonitis in sheep. It is known as visna when found in the brain, and maedi when infecting the lungs. Lifelong, persistent infections in sheep occur in the lungs, lymph nodes, spleen, joints, central nervous system, and mammary glands; The condition is sometimes known as ovine progressive pneumonia (OPP), particularly in the United States, or Montana sheep disease. White blood cells of the monocyte/macrophage lineage are the main target of the virus.

Gyrovirus is a genus of viruses, in the family Anelloviridae. Until 2011, chicken anemia virus was the only Gyrovirus identified, but since then gyroviruses have also been identified in humans. Diseases associated with this genus include: chicken infectious anemia, which is associated with depletion of cortical thymocytes and erythroblastoid cells.

<span class="mw-page-title-main">Late protein</span>

A late protein is a viral protein that is formed after replication of the virus. One example is VP4 from simian virus 40 (SV40).

Bocaparvovirus is a genus of viruses in the subfamily Parvovirinae of the virus family Parvoviridae. Humans, cattle, and dogs serve as natural hosts. There are 28 species in this genus. Diseases associated with this genus include, in humans, acute respiratory illness, and in cattle, diarrhea and mild respiratory symptoms.

Densovirinae is a subfamily of single-stranded DNA viruses in the family Parvoviridae. The subfamily has 11 recognized genera and 21 species. Densoviruses are known to infect members of insect orders Blattodea, Diptera, Hemiptera, Hymenoptera, Lepidoptera, and Orthoptera, while some viruses infect and multiply in crustaceans such as shrimp or crayfish, or sea stars from phylum Echinodermata.

Tetraparvovirus are a genus of viruses in the family Parvoviridae. There are six recognized species: Chiropteran tetraparvovirus 1, Primate tetraparvovirus 1, Ungulate tetraparvovirus 1, Ungulate tetraparvovirus 2, Ungulate tetraparvovirus 3, and Ungulate tetraparvovirus 4.

<span class="mw-page-title-main">Minute virus of mice</span> Virus

Minute virus of mice (MVM) is the exemplar virus of the species Rodent protoparvovirus 1, in the genus Protoparvovirus of the Parvoviridae family of viruses. MVM exists in multiple variant forms including MVMp, which is the prototype strain that infects cells of fibroblast origin, while MVMi, the immunosuppressive strain, infects T lymphocytes. MVM is a common infection in laboratory mice due to its highly contagious nature. The virus can be shed from infected mice via feces and urine, but also via fomites and nasal secretions. Typically there are no clinical signs of infection in adult mice, however, experimental infection can cause multiple organ damage during fetal development or shortly after birth.

<i>Protoparvovirus</i> Genus of viruses

Protoparvovirus is a genus of viruses in the Parvovirinae subfamily of the virus family Parvoviridae. Vertebrates serve as natural hosts. There are 15 species in the genus including Rodent protoparvovirus 1 for which the exemplar virus is minute virus of mice (MVM). This genus also includes canine parvovirus (CPV), which causes gastrointestinal tract damage in puppies that is about 80% fatal, and porcine parvovirus (PPV), which is a major cause of fetal death and infertility in pigs. The genus divides phylogenetically into two branches, one that contains many founder members of the family, such as MVM, CPV and PPV, which have been studied in considerable detail, and a second branch occupied exclusively by predicted viruses whose coding sequences were identified recently in the wild using virus discovery approaches, but whose biology remains minimally explored. This second branch currently contains two species whose members infect humans, called Primate protoparvovirus 1 and Primate protoparvovirus 3. Until 2014, the genus was called Parvovirus, but it was renamed to eliminate confusion between members of this genus and members of the entire family Parvoviridae.

WU polyomavirus is a virus of the family Polyomaviridae. It was discovered in 2007 in samples of human respiratory secretions, originally from a child patient in Australia who presented with clinical signs of pneumonia and in whom other common respiratory viruses were not detected. Follow-up studies identified the presence of WU virus in respiratory secretion samples from patients in Australia and the United States, suggesting that, like other human polyomaviruses, WU virus is widely distributed.

Minor capsid protein VP2 and minor capsid protein VP3 are viral proteins that are components of the polyomavirus capsid. Polyomavirus capsids are composed of three proteins; the major component is major capsid protein VP1, which self-assembles into pentamers that in turn self-assemble into enclosed icosahedral structures. The minor components are VP2 and VP3, which bind in the interior of the capsid.

Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family Parvoviridae. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes in which the coding portion of the genome is flanked by telomeres at each end that form hairpin loops. During RHR, these hairpin loops repeatedly unfold and refold to change the direction of DNA replication so that replication progresses in a continuous manner back and forth across the genome. RHR is initiated and terminated by an endonuclease encoded by parvoviruses that is variously called NS1 or Rep, and RHR is similar to rolling circle replication, which is used by ssDNA viruses that have circular genomes.

References

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  32. ↑ Ursic T, Steyer A, Kopriva S, Kalan G, Krivec U, Petrovec M (2011). "Human bocavirus as the cause of a life-threatening infection". J. Clin. Microbiol. 49 (3): 1179–81. doi:10.1128/JCM.02362-10. PMC   3067724 . PMID   21227992.
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